Workflow: 02-peakcall.cwl
Fetched 2024-04-16 21:26:19 GMT
Verified with cwltool version 3.1.20221201130942
DNase-seq 02 quantification
- Selected
- |
- Default Values
- Nested Workflows
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| nthreads | Integer | ||
| input_bam_files | File[] | ||
| input_bam_format | String |
BAM or BAMPE for single-end and paired-end reads respectively (default: BAM) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| spp |
../spp/spp.cwl
(CommandLineTool)
|
||
| count-peaks |
../utils/count-with-output-suffix.cwl
(CommandLineTool)
|
Counts lines in a file and returns a suffixed file with that number |
|
| peak-calling-narrow |
../peak_calling/macs2-callpeak.cwl
(CommandLineTool)
|
||
| count-reads-filtered |
../peak_calling/count-reads-after-filtering.cwl
(CommandLineTool)
|
Count number of dedup-ed reads used in peak calling |
|
| filter-reads-in-peaks |
../peak_calling/samtools-filter-in-bedfile.cwl
(CommandLineTool)
|
Filter BAM file to only include reads overlapping with a BED file |
|
| extract-peak-frag-length |
../spp/extract-best-frag-length.cwl
(CommandLineTool)
|
Extracts best fragment length from SPP output text file |
|
| extract-count-reads-in-peaks |
../peak_calling/samtools-extract-number-mapped-reads.cwl
(CommandLineTool)
|
Extract mapped reads from BAM file using Samtools flagstat command |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_peak_xls_file | File[] |
Peak calling report file (*_peaks.xls file produced by MACS2) |
|
| output_narrowpeak_file | File[] |
peakshift/phantomPeak results file |
|
| output_spp_x_cross_corr | File[] |
peakshift/phantomPeak results file |
|
| output_spp_cross_corr_plot | File[] |
peakshift/phantomPeak results file |
|
| output_extended_narrowpeak_file | File[] |
peakshift/phantomPeak extended fragment results file |
|
| output_filtered_read_count_file | File[] |
Filtered read count reported by MACS2 |
|
| output_peak_count_within_replicate | File[] |
Peak counts within replicate |
|
| output_read_in_peak_count_within_replicate | File[] |
Peak counts within replicate |
Permalink:
https://w3id.org/cwl/view/git/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/DNase-seq_pipeline/02-peakcall.cwl
